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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-04-22, 22:47 AEST based on data in: /fast/sci-irc/eliott_wgs/hpc/movp/work/a0/aba86270b44e0881a4d81fe7007b3f


        General Statistics

        Showing 346/346 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        CSUD006_S1_L004_R1_001
        31.9%
        40%
        66.7
        CSUD006_S1_L004_R2_001
        30.9%
        40%
        66.7
        CSUD008_S2_L004_R1_001
        35.3%
        40%
        92.3
        CSUD008_S2_L004_R2_001
        34.1%
        40%
        92.3
        CSUD010_S3_L004_R1_001
        32.0%
        40%
        74.7
        CSUD010_S3_L004_R2_001
        30.3%
        41%
        74.7
        CSUD014_S4_L004_R1_001
        33.0%
        40%
        76.6
        CSUD014_S4_L004_R2_001
        30.9%
        41%
        76.6
        CSUD018_S5_L004_R1_001
        34.5%
        40%
        90.3
        CSUD018_S5_L004_R2_001
        33.3%
        40%
        90.3
        CSUD074_S6_L004_R1_001
        34.9%
        40%
        94.1
        CSUD074_S6_L004_R2_001
        33.7%
        40%
        94.1
        CSUD076_S7_L004_R1_001
        36.0%
        41%
        90.1
        CSUD076_S7_L004_R2_001
        34.8%
        41%
        90.1
        CSUD079_S8_L004_R1_001
        33.2%
        40%
        77.1
        CSUD079_S8_L004_R2_001
        31.8%
        40%
        77.1
        CSUD085_S9_L004_R1_001
        32.7%
        40%
        67.7
        CSUD085_S9_L004_R2_001
        31.9%
        40%
        67.7
        CTON061_S10_L004_R1_001
        32.6%
        40%
        81.7
        CTON061_S10_L004_R2_001
        31.0%
        40%
        81.7
        CTON062_S5_L001_R1_001
        13.4%
        40%
        28.2
        CTON062_S5_L001_R2_001
        13.6%
        40%
        28.2
        CTON062_S5_L002_R1_001
        14.2%
        40%
        28.8
        CTON062_S5_L002_R2_001
        14.7%
        40%
        28.8
        CTON062_S5_L003_R1_001
        15.7%
        40%
        29.4
        CTON062_S5_L003_R2_001
        16.0%
        40%
        29.4
        CTON065_S11_L004_R1_001
        31.0%
        41%
        66.8
        CTON065_S11_L004_R2_001
        30.2%
        41%
        66.8
        CTON066_S26_L001_R1_001
        13.4%
        40%
        27.0
        CTON066_S26_L001_R2_001
        13.7%
        41%
        27.0
        CTON066_S26_L002_R1_001
        14.6%
        40%
        27.5
        CTON066_S26_L002_R2_001
        15.1%
        41%
        27.5
        CTON066_S26_L003_R1_001
        16.4%
        40%
        28.5
        CTON066_S26_L003_R2_001
        16.7%
        41%
        28.5
        CTON068_S12_L004_R1_001
        33.7%
        40%
        90.9
        CTON068_S12_L004_R2_001
        32.5%
        41%
        90.9
        CTON069_S13_L004_R1_001
        27.0%
        40%
        45.5
        CTON069_S13_L004_R2_001
        26.2%
        41%
        45.5
        CTON110_S14_L004_R1_001
        34.0%
        40%
        85.7
        CTON110_S14_L004_R2_001
        32.6%
        40%
        85.7
        CTONO60_S15_L004_R1_001
        33.7%
        40%
        84.9
        CTONO60_S15_L004_R2_001
        32.9%
        40%
        84.9
        CVLA044_S23_L001_R1_001
        14.0%
        41%
        28.6
        CVLA044_S23_L001_R2_001
        14.0%
        41%
        28.6
        CVLA044_S23_L002_R1_001
        15.1%
        40%
        29.3
        CVLA044_S23_L002_R2_001
        15.4%
        41%
        29.3
        CVLA044_S23_L003_R1_001
        17.0%
        40%
        30.0
        CVLA044_S23_L003_R2_001
        17.2%
        41%
        30.0
        CVLA045_S16_L004_R1_001
        33.6%
        40%
        83.1
        CVLA045_S16_L004_R2_001
        30.5%
        40%
        83.1
        CVLA046_S17_L004_R1_001
        34.3%
        40%
        86.6
        CVLA046_S17_L004_R2_001
        33.2%
        40%
        86.6
        CVLA047_S18_L004_R1_001
        34.7%
        40%
        84.8
        CVLA047_S18_L004_R2_001
        34.0%
        40%
        84.8
        CVLA053_S19_L004_R1_001
        36.6%
        40%
        101.3
        CVLA053_S19_L004_R2_001
        34.9%
        40%
        101.3
        CVLA057_S20_L004_R1_001
        34.8%
        41%
        90.9
        CVLA057_S20_L004_R2_001
        33.7%
        41%
        90.9
        CVLA098_S40_L001_R1_001
        13.1%
        40%
        25.0
        CVLA098_S40_L001_R2_001
        13.4%
        41%
        25.0
        CVLA098_S40_L002_R1_001
        13.8%
        40%
        25.5
        CVLA098_S40_L002_R2_001
        14.4%
        41%
        25.5
        CVLA098_S40_L003_R1_001
        15.3%
        40%
        26.2
        CVLA098_S40_L003_R2_001
        15.8%
        41%
        26.2
        CVLA104_S21_L004_R1_001
        35.7%
        40%
        95.0
        CVLA104_S21_L004_R2_001
        34.1%
        40%
        95.0
        LCHA114_S22_L004_R1_001
        32.3%
        40%
        74.9
        LCHA114_S22_L004_R2_001
        30.8%
        41%
        74.9
        LCHA118_S11_L001_R1_001
        14.2%
        40%
        30.9
        LCHA118_S11_L001_R2_001
        14.1%
        41%
        30.9
        LCHA118_S11_L002_R1_001
        15.5%
        40%
        31.6
        LCHA118_S11_L002_R2_001
        15.7%
        41%
        31.6
        LCHA118_S11_L003_R1_001
        17.3%
        40%
        32.5
        LCHA118_S11_L003_R2_001
        17.4%
        41%
        32.5
        LCHA119_S23_L004_R1_001
        34.7%
        40%
        88.4
        LCHA119_S23_L004_R2_001
        34.0%
        40%
        88.4
        LCHA120_S21_L001_R1_001
        13.5%
        41%
        26.4
        LCHA120_S21_L001_R2_001
        13.8%
        41%
        26.4
        LCHA120_S21_L002_R1_001
        14.6%
        41%
        26.7
        LCHA120_S21_L002_R2_001
        14.8%
        41%
        26.7
        LCHA120_S21_L003_R1_001
        16.1%
        41%
        27.5
        LCHA120_S21_L003_R2_001
        16.2%
        41%
        27.5
        LCHA123_S9_L001_R1_001
        14.2%
        41%
        29.0
        LCHA123_S9_L001_R2_001
        14.2%
        42%
        29.0
        LCHA123_S9_L002_R1_001
        15.1%
        41%
        29.7
        LCHA123_S9_L002_R2_001
        15.6%
        42%
        29.7
        LCHA123_S9_L003_R1_001
        16.6%
        41%
        30.1
        LCHA123_S9_L003_R2_001
        16.9%
        42%
        30.1
        LCHA135_S24_L004_R1_001
        36.1%
        40%
        95.4
        LCHA135_S24_L004_R2_001
        35.1%
        40%
        95.4
        LCHA136_S25_L004_R1_001
        34.6%
        40%
        92.7
        LCHA136_S25_L004_R2_001
        33.0%
        40%
        92.7
        LCHA138_S26_L004_R1_001
        30.7%
        40%
        68.9
        LCHA138_S26_L004_R2_001
        29.1%
        40%
        68.9
        LCKM154_S27_L004_R1_001
        31.7%
        40%
        71.8
        LCKM154_S27_L004_R2_001
        30.5%
        40%
        71.8
        LCKM158_S28_L004_R1_001
        34.9%
        40%
        91.3
        LCKM158_S28_L004_R2_001
        33.8%
        40%
        91.3
        LCKM163_S29_L004_R1_001
        32.2%
        40%
        60.8
        LCKM163_S29_L004_R2_001
        31.2%
        40%
        60.8
        LCKM165_S30_L004_R1_001
        33.7%
        40%
        80.0
        LCKM165_S30_L004_R2_001
        32.8%
        41%
        80.0
        LCKM166_S31_L004_R1_001
        31.3%
        40%
        69.4
        LCKM166_S31_L004_R2_001
        31.3%
        41%
        69.4
        LCKM174_S32_L004_R1_001
        36.0%
        40%
        104.3
        LCKM174_S32_L004_R2_001
        34.5%
        40%
        104.3
        LCKM176_S33_L004_R1_001
        32.8%
        40%
        74.3
        LCKM176_S33_L004_R2_001
        31.8%
        41%
        74.3
        LCKM180_S34_L004_R1_001
        32.8%
        40%
        83.0
        LCKM180_S34_L004_R2_001
        31.4%
        40%
        83.0
        LHER700_S22_L001_R1_001
        13.9%
        40%
        30.1
        LHER700_S22_L001_R2_001
        14.1%
        40%
        30.1
        LHER700_S22_L002_R1_001
        15.0%
        40%
        30.8
        LHER700_S22_L002_R2_001
        15.6%
        40%
        30.8
        LHER700_S22_L003_R1_001
        16.7%
        40%
        31.6
        LHER700_S22_L003_R2_001
        16.9%
        40%
        31.6
        LHER701_S37_L001_R1_001
        14.1%
        40%
        27.5
        LHER701_S37_L001_R2_001
        14.0%
        40%
        27.5
        LHER701_S37_L002_R1_001
        15.0%
        40%
        28.2
        LHER701_S37_L002_R2_001
        15.1%
        40%
        28.2
        LHER701_S37_L003_R1_001
        16.4%
        40%
        28.7
        LHER701_S37_L003_R2_001
        16.4%
        40%
        28.7
        LHER702_S17_L001_R1_001
        14.9%
        40%
        30.8
        LHER702_S17_L001_R2_001
        15.1%
        41%
        30.8
        LHER702_S17_L002_R1_001
        15.9%
        40%
        31.1
        LHER702_S17_L002_R2_001
        16.4%
        41%
        31.1
        LHER702_S17_L003_R1_001
        17.7%
        40%
        32.4
        LHER702_S17_L003_R2_001
        18.1%
        41%
        32.4
        LHER703_S19_L001_R1_001
        14.3%
        40%
        27.9
        LHER703_S19_L001_R2_001
        14.8%
        41%
        27.9
        LHER703_S19_L002_R1_001
        15.6%
        40%
        28.5
        LHER703_S19_L002_R2_001
        16.3%
        41%
        28.5
        LHER703_S19_L003_R1_001
        17.4%
        40%
        29.7
        LHER703_S19_L003_R2_001
        17.9%
        41%
        29.7
        LHER704_S7_L001_R1_001
        13.8%
        40%
        27.7
        LHER704_S7_L001_R2_001
        14.1%
        41%
        27.7
        LHER704_S7_L002_R1_001
        14.8%
        40%
        28.4
        LHER704_S7_L002_R2_001
        15.3%
        40%
        28.4
        LHER704_S7_L003_R1_001
        16.3%
        40%
        29.3
        LHER704_S7_L003_R2_001
        16.9%
        41%
        29.3
        LHER705_S4_L001_R1_001
        14.2%
        40%
        27.4
        LHER705_S4_L001_R2_001
        14.7%
        41%
        27.4
        LHER705_S4_L002_R1_001
        15.5%
        40%
        28.0
        LHER705_S4_L002_R2_001
        16.0%
        41%
        28.0
        LHER705_S4_L003_R1_001
        17.3%
        40%
        29.1
        LHER705_S4_L003_R2_001
        17.7%
        41%
        29.1
        LHER706_S25_L001_R1_001
        14.3%
        40%
        25.4
        LHER706_S25_L001_R2_001
        14.6%
        40%
        25.4
        LHER706_S25_L002_R1_001
        15.3%
        40%
        26.1
        LHER706_S25_L002_R2_001
        15.7%
        40%
        26.1
        LHER706_S25_L003_R1_001
        17.1%
        40%
        27.1
        LHER706_S25_L003_R2_001
        17.3%
        40%
        27.1
        LHER707_S6_L001_R1_001
        14.5%
        40%
        27.1
        LHER707_S6_L001_R2_001
        14.8%
        41%
        27.1
        LHER707_S6_L002_R1_001
        15.6%
        40%
        27.5
        LHER707_S6_L002_R2_001
        16.1%
        41%
        27.5
        LHER707_S6_L003_R1_001
        17.5%
        40%
        28.8
        LHER707_S6_L003_R2_001
        17.8%
        41%
        28.8
        LKES142_S35_L004_R1_001
        32.4%
        40%
        73.9
        LKES142_S35_L004_R2_001
        31.3%
        41%
        73.9
        LKES143_S36_L004_R1_001
        34.3%
        40%
        92.8
        LKES143_S36_L004_R2_001
        33.2%
        40%
        92.8
        LKES145_S37_L004_R1_001
        33.6%
        40%
        69.4
        LKES145_S37_L004_R2_001
        32.9%
        40%
        69.4
        LKES148_S16_L001_R1_001
        14.1%
        40%
        29.4
        LKES148_S16_L001_R2_001
        14.2%
        41%
        29.4
        LKES148_S16_L002_R1_001
        15.5%
        40%
        30.2
        LKES148_S16_L002_R2_001
        15.7%
        41%
        30.2
        LKES148_S16_L003_R1_001
        17.2%
        40%
        31.0
        LKES148_S16_L003_R2_001
        17.3%
        41%
        31.0
        LKES149_S45_L001_R1_001
        13.6%
        40%
        27.4
        LKES149_S45_L001_R2_001
        13.7%
        40%
        27.4
        LKES149_S45_L002_R1_001
        14.6%
        40%
        28.1
        LKES149_S45_L002_R2_001
        14.9%
        40%
        28.1
        LKES149_S45_L003_R1_001
        16.4%
        40%
        28.7
        LKES149_S45_L003_R2_001
        16.3%
        40%
        28.7
        LKES169_S44_L001_R1_001
        14.4%
        40%
        29.5
        LKES169_S44_L001_R2_001
        14.4%
        41%
        29.5
        LKES169_S44_L002_R1_001
        15.3%
        40%
        29.7
        LKES169_S44_L002_R2_001
        15.5%
        41%
        29.7
        LKES169_S44_L003_R1_001
        17.1%
        40%
        30.8
        LKES169_S44_L003_R2_001
        17.3%
        41%
        30.8
        LKES170_S35_L001_R1_001
        14.3%
        41%
        30.0
        LKES170_S35_L001_R2_001
        14.2%
        41%
        30.0
        LKES170_S35_L002_R1_001
        15.4%
        41%
        30.8
        LKES170_S35_L002_R2_001
        15.6%
        41%
        30.8
        LKES170_S35_L003_R1_001
        17.1%
        41%
        31.7
        LKES170_S35_L003_R2_001
        17.2%
        41%
        31.7
        LKES172_S38_L004_R1_001
        33.4%
        40%
        83.6
        LKES172_S38_L004_R2_001
        32.7%
        40%
        83.6
        LSBI021_S1_L001_R1_001
        14.1%
        41%
        28.2
        LSBI021_S1_L001_R2_001
        14.6%
        42%
        28.2
        LSBI021_S1_L002_R1_001
        15.2%
        41%
        28.2
        LSBI021_S1_L002_R2_001
        16.0%
        42%
        28.2
        LSBI021_S1_L003_R1_001
        16.9%
        41%
        29.8
        LSBI021_S1_L003_R2_001
        17.6%
        42%
        29.8
        LSBI023_S39_L001_R1_001
        14.5%
        40%
        33.3
        LSBI023_S39_L001_R2_001
        14.9%
        41%
        33.3
        LSBI023_S39_L002_R1_001
        15.9%
        40%
        34.1
        LSBI023_S39_L002_R2_001
        16.3%
        41%
        34.1
        LSBI023_S39_L003_R1_001
        17.7%
        40%
        35.0
        LSBI023_S39_L003_R2_001
        17.9%
        41%
        35.0
        LSBI024_S2_L001_R1_001
        13.6%
        41%
        31.4
        LSBI024_S2_L001_R2_001
        13.9%
        41%
        31.4
        LSBI024_S2_L002_R1_001
        14.3%
        41%
        32.0
        LSBI024_S2_L002_R2_001
        15.0%
        41%
        32.0
        LSBI024_S2_L003_R1_001
        16.0%
        41%
        32.7
        LSBI024_S2_L003_R2_001
        16.3%
        41%
        32.7
        LSBI027_S32_L001_R1_001
        13.8%
        40%
        28.5
        LSBI027_S32_L001_R2_001
        14.4%
        40%
        28.5
        LSBI027_S32_L002_R1_001
        15.0%
        40%
        29.2
        LSBI027_S32_L002_R2_001
        15.6%
        40%
        29.2
        LSBI027_S32_L003_R1_001
        16.7%
        40%
        30.1
        LSBI027_S32_L003_R2_001
        17.2%
        40%
        30.1
        LSBI032_S33_L001_R1_001
        12.9%
        40%
        24.0
        LSBI032_S33_L001_R2_001
        13.6%
        41%
        24.0
        LSBI032_S33_L002_R1_001
        14.1%
        40%
        24.4
        LSBI032_S33_L002_R2_001
        14.8%
        41%
        24.4
        LSBI032_S33_L003_R1_001
        15.8%
        40%
        25.3
        LSBI032_S33_L003_R2_001
        16.4%
        41%
        25.3
        LSBI034_S41_L001_R1_001
        14.0%
        42%
        29.2
        LSBI034_S41_L001_R2_001
        13.6%
        42%
        29.2
        LSBI034_S41_L002_R1_001
        14.6%
        41%
        29.9
        LSBI034_S41_L002_R2_001
        14.5%
        42%
        29.9
        LSBI034_S41_L003_R1_001
        16.0%
        41%
        30.2
        LSBI034_S41_L003_R2_001
        15.8%
        42%
        30.2
        LSBI036_S14_L001_R1_001
        13.6%
        41%
        25.5
        LSBI036_S14_L001_R2_001
        14.0%
        41%
        25.5
        LSBI036_S14_L002_R1_001
        14.7%
        41%
        25.8
        LSBI036_S14_L002_R2_001
        15.2%
        41%
        25.8
        LSBI036_S14_L003_R1_001
        16.4%
        40%
        26.7
        LSBI036_S14_L003_R2_001
        16.8%
        41%
        26.7
        LSBI040_S36_L001_R1_001
        13.9%
        40%
        27.8
        LSBI040_S36_L001_R2_001
        14.3%
        41%
        27.8
        LSBI040_S36_L002_R1_001
        15.0%
        40%
        28.4
        LSBI040_S36_L002_R2_001
        15.5%
        41%
        28.4
        LSBI040_S36_L003_R1_001
        16.9%
        40%
        29.5
        LSBI040_S36_L003_R2_001
        17.4%
        41%
        29.5
        TDDT720_S31_L001_R1_001
        15.3%
        40%
        36.5
        TDDT720_S31_L001_R2_001
        15.4%
        41%
        36.5
        TDDT720_S31_L002_R1_001
        16.1%
        40%
        37.5
        TDDT720_S31_L002_R2_001
        16.5%
        41%
        37.5
        TDDT720_S31_L003_R1_001
        17.5%
        40%
        38.5
        TDDT720_S31_L003_R2_001
        17.9%
        41%
        38.5
        TDUG708_S30_L001_R1_001
        13.8%
        40%
        29.9
        TDUG708_S30_L001_R2_001
        14.3%
        41%
        29.9
        TDUG708_S30_L002_R1_001
        15.0%
        40%
        30.5
        TDUG708_S30_L002_R2_001
        15.5%
        41%
        30.5
        TDUG708_S30_L003_R1_001
        16.9%
        40%
        31.3
        TDUG708_S30_L003_R2_001
        17.2%
        41%
        31.3
        TDUG709_S28_L001_R1_001
        13.5%
        40%
        28.1
        TDUG709_S28_L001_R2_001
        14.4%
        41%
        28.1
        TDUG709_S28_L002_R1_001
        14.3%
        40%
        28.6
        TDUG709_S28_L002_R2_001
        15.5%
        41%
        28.6
        TDUG709_S28_L003_R1_001
        16.0%
        40%
        29.7
        TDUG709_S28_L003_R2_001
        17.1%
        41%
        29.7
        TDUG710_S10_L001_R1_001
        14.1%
        40%
        29.8
        TDUG710_S10_L001_R2_001
        14.8%
        41%
        29.8
        TDUG710_S10_L002_R1_001
        15.3%
        40%
        30.4
        TDUG710_S10_L002_R2_001
        16.0%
        41%
        30.4
        TDUG710_S10_L003_R1_001
        17.1%
        40%
        31.6
        TDUG710_S10_L003_R2_001
        17.8%
        41%
        31.6
        TDUG711_S29_L001_R1_001
        13.4%
        40%
        28.8
        TDUG711_S29_L001_R2_001
        13.6%
        41%
        28.8
        TDUG711_S29_L002_R1_001
        14.4%
        40%
        29.4
        TDUG711_S29_L002_R2_001
        14.8%
        41%
        29.4
        TDUG711_S29_L003_R1_001
        15.9%
        40%
        30.1
        TDUG711_S29_L003_R2_001
        16.2%
        41%
        30.1
        TDUG712_S18_L001_R1_001
        13.0%
        41%
        22.1
        TDUG712_S18_L001_R2_001
        13.1%
        41%
        22.1
        TDUG712_S18_L002_R1_001
        14.2%
        41%
        22.7
        TDUG712_S18_L002_R2_001
        14.3%
        41%
        22.7
        TDUG712_S18_L003_R1_001
        15.4%
        41%
        23.0
        TDUG712_S18_L003_R2_001
        15.5%
        41%
        23.0
        TDUG713_S8_L001_R1_001
        15.4%
        40%
        37.3
        TDUG713_S8_L001_R2_001
        15.5%
        41%
        37.3
        TDUG713_S8_L002_R1_001
        16.1%
        40%
        38.0
        TDUG713_S8_L002_R2_001
        16.6%
        41%
        38.0
        TDUG713_S8_L003_R1_001
        17.9%
        40%
        38.9
        TDUG713_S8_L003_R2_001
        18.0%
        41%
        38.9
        TDUG714_S24_L001_R1_001
        14.2%
        40%
        28.9
        TDUG714_S24_L001_R2_001
        14.2%
        41%
        28.9
        TDUG714_S24_L002_R1_001
        15.1%
        40%
        29.7
        TDUG714_S24_L002_R2_001
        15.3%
        41%
        29.7
        TDUG714_S24_L003_R1_001
        16.6%
        40%
        30.4
        TDUG714_S24_L003_R2_001
        16.8%
        41%
        30.4
        TDXT718_S3_L001_R1_001
        15.1%
        40%
        32.1
        TDXT718_S3_L001_R2_001
        14.8%
        40%
        32.1
        TDXT718_S3_L002_R1_001
        16.6%
        40%
        32.9
        TDXT718_S3_L002_R2_001
        16.4%
        40%
        32.9
        TDXT718_S3_L003_R1_001
        18.5%
        40%
        34.2
        TDXT718_S3_L003_R2_001
        17.9%
        40%
        34.2
        TKXT719_S15_L001_R1_001
        13.6%
        40%
        28.9
        TKXT719_S15_L001_R2_001
        13.7%
        41%
        28.9
        TKXT719_S15_L002_R1_001
        14.7%
        40%
        29.5
        TKXT719_S15_L002_R2_001
        14.9%
        41%
        29.5
        TKXT719_S15_L003_R1_001
        16.1%
        40%
        30.3
        TKXT719_S15_L003_R2_001
        16.2%
        41%
        30.3
        TTTD721_S27_L001_R1_001
        14.4%
        40%
        35.4
        TTTD721_S27_L001_R2_001
        14.8%
        41%
        35.4
        TTTD721_S27_L002_R1_001
        15.2%
        40%
        36.2
        TTTD721_S27_L002_R2_001
        16.0%
        41%
        36.2
        TTTD721_S27_L003_R1_001
        16.8%
        40%
        37.2
        TTTD721_S27_L003_R2_001
        17.4%
        41%
        37.2
        TTWN717_S43_L001_R1_001
        15.0%
        41%
        37.9
        TTWN717_S43_L001_R2_001
        15.1%
        41%
        37.9
        TTWN717_S43_L002_R1_001
        15.6%
        41%
        38.5
        TTWN717_S43_L002_R2_001
        16.3%
        41%
        38.5
        TTWN717_S43_L003_R1_001
        16.9%
        41%
        39.1
        TTWN717_S43_L003_R2_001
        17.4%
        41%
        39.1
        TTWN722_S42_L001_R1_001
        14.3%
        40%
        28.9
        TTWN722_S42_L001_R2_001
        14.4%
        40%
        28.9
        TTWN722_S42_L002_R1_001
        15.1%
        40%
        29.5
        TTWN722_S42_L002_R2_001
        15.3%
        40%
        29.5
        TTWN722_S42_L003_R1_001
        16.6%
        40%
        29.4
        TTWN722_S42_L003_R2_001
        16.7%
        40%
        29.4
        TTWN723_S38_L001_R1_001
        15.0%
        40%
        36.9
        TTWN723_S38_L001_R2_001
        14.9%
        41%
        36.9
        TTWN723_S38_L002_R1_001
        15.7%
        40%
        37.7
        TTWN723_S38_L002_R2_001
        16.1%
        41%
        37.7
        TTWN723_S38_L003_R1_001
        17.2%
        40%
        38.4
        TTWN723_S38_L003_R2_001
        17.4%
        41%
        38.4
        TTWN724_S20_L001_R1_001
        13.8%
        40%
        30.0
        TTWN724_S20_L001_R2_001
        13.9%
        41%
        30.0
        TTWN724_S20_L002_R1_001
        15.0%
        40%
        30.8
        TTWN724_S20_L002_R2_001
        15.0%
        41%
        30.8
        TTWN724_S20_L003_R1_001
        16.4%
        40%
        31.4
        TTWN724_S20_L003_R2_001
        16.4%
        41%
        31.4
        XRHQ997_S13_L001_R1_001
        13.5%
        41%
        27.7
        XRHQ997_S13_L001_R2_001
        13.4%
        41%
        27.7
        XRHQ997_S13_L002_R1_001
        14.2%
        41%
        28.4
        XRHQ997_S13_L002_R2_001
        14.6%
        41%
        28.4
        XRHQ997_S13_L003_R1_001
        15.8%
        41%
        29.2
        XRHQ997_S13_L003_R2_001
        16.1%
        41%
        29.2
        XRHQ998_S12_L001_R1_001
        13.4%
        40%
        30.0
        XRHQ998_S12_L001_R2_001
        14.0%
        41%
        30.0
        XRHQ998_S12_L002_R1_001
        14.3%
        40%
        30.6
        XRHQ998_S12_L002_R2_001
        15.1%
        41%
        30.6
        XRHQ998_S12_L003_R1_001
        15.9%
        40%
        31.4
        XRHQ998_S12_L003_R2_001
        16.5%
        41%
        31.4
        XRHQ999_S34_L001_R1_001
        13.8%
        40%
        28.0
        XRHQ999_S34_L001_R2_001
        14.4%
        41%
        28.0
        XRHQ999_S34_L002_R1_001
        14.8%
        40%
        28.7
        XRHQ999_S34_L002_R2_001
        15.5%
        41%
        28.7
        XRHQ999_S34_L003_R1_001
        16.6%
        40%
        29.6
        XRHQ999_S34_L003_R2_001
        17.3%
        41%
        29.6

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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